Hi All, I would like to restrain the COM of a molecule, say a protein, in my simulation. I found the pull code can do the job. However, I am not sure about several parameters in the .mdp file.
For example, if I want to restrain the COM of the protein in only z direction, but not rigidly, I can specify the following parameters: *; Setting A* *pull = umbrella* *pull-geometry = position* *pull-dim = N N Y ; only applied to Z direction* *pull-ngroups = 1 * *pull-group1 = Protein* *pull-start = no* *pull-init1 = 3.0 3.0 3.0 ; suppose the initial position of the COM is 3.0 3.0 3.0* *pull-k1 = 50* I am not confident about my understanding of the settings. Here I didn't specify *pull-group0*. Therefore the position of the reference point is 0.0 0.0 0.0. But *pull-init1* moves the reference point to *3.0 3.0 3.0. *I don't know the reasonable range for *pull-k1 *too. I want the COM can only have a small deviation from its initial position. Is 50 too large or too small? And I figured out another approach. *; Setting B* *pull = umbrella* *pull-geometry = position* *pull-dim = N N Y ; only applied to Z direction* *pull-ngroups = 1 * *pull-group1 = Protein* *pull-start = yes* *pull-k1 = 50* * * The GROMACS manual says *pull-start=yes *adds the COM distance of the starting conformation to *pull-init. *Does it mean Setting B is equivalent to Setting A? If I set *pull-geometry= position, *does *pull-start=yes *add the initial position of the COM to *pull-init* as a vector? If it's true, then I don't need to calculate the initial position of the COM. Thanks a lot. Best Bin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
